Shadow Pokemon Return Version 2
by Auramaster24
Summary: Giovanni is using Shadow pokemon in his attempt for world domintion. Can Ash bring him down or is the world doomd to giovanni's tyranny? Pokeshipping and Auraauquashipping  oc and Lily Waterflower
1. Enter Shadow And Eclipse

Enter Shadow and Eclipse

Disclaimer: I don't own Pokemon, I do own Joel. Definitions will be in bold.

Ash- 15

Joel-21

Misty-15

Delia(Mrs. Ketchum)- 45

Giovanni- 48

After losing in the semifinals of the Sinnoh league, Ash Ketchum has left into solitary training. It has been 3 months had no one has seen or heard from him since. Now Team Rocket has threatened the world with "Shadow Pokemon". Pokemon whose hearts have been artificially shut and evil.

Giovanni, Leader of team rocket, hopes to lure Ash Ketchum out of hiding. He has captured Ash's mother Delia Ketchum, His secret crush, Misty Waterflower. Delia was a tall woman with long auburn hair and light brown eyes. Misty had given up her ponytail and grew her red hair to her shoulders. She had sea green eyes that were filled with worry for Ash.

Every night, The guards who guarded them would play the Pokemon card game to pass the time. They heard things about two trainers called Shadow and Eclipse. They had gotten in Giovanni's way and he had a feeling he knew who they really are.. Tonight they would hear the rumor..

"You think it's true? About Shadow and Eclipse?"

"You mean them really being Ketchum and Berlitz?"

Delia and Misty looked at each other..

'_Ketchum.. Ash..'_

" Lucario, Aura Sphere!"

" Storm, Shadow Ball!"

The Aura Sphere blew the door off its hinges while the Shadow Ball knocked the two guard unconscious.

They look out their cells to see two figures standing in the doorway to the dungeon. One wore a light blue cloak, blue jeans and a dark blue long sleeve shirt. He was tall, seemed about 5 foot 11 inches. He wore a Silver mask that covered all but his blue eyes. The eyes of a proud beast. In front of him was a medium dog like Pokemon. Blue in color. It had a mermaid like tail, Ears that resembled fins. And a fin on its head. It also had white collar like appendage around its head. This Pokemon was a Vaporeon.

The other was about 5 foot 5 inches. He also wore a cloak but this one was dark blue. His blue jeans he wore were ripped as if he been through a lot. His shirt was a plain white. Like his friend, he also wore a silver mask. Underneath the mask they could see chocolate brown eyes. Underneath his hood they could see raven colored hair. In front of him was a tall blue Pokemon with a yellowish white furred chest. Black legs, hands and marking around it's face. It also had medium length blue ears. This Pokemon's name is Lucario.

" I don't like this Eclipse. It was too easy getting here." the shorter told the taller in a worried voice.

" You have learned well. My apprentice. " Eclipse told Shadow. It was then that Shadow had noticed the were being watched.

' Oh no' Shadow thought.

" Eclipse, We have company.."

Eclipse noticed the prisoners..

'_This complicates things a bit..'_ He thought..

As Shadow and Eclipse had begun to Mrs. Ketchum and Misty, a female voice came over the speaker system.

" Attention all units! Attention all units! Aura Knight alert.. Priority one.."

"Wow, Priority one. Don't I feel special." Shadow marveled. Eclipse slapped him on the back of the head.

"Ouch."

" Shadow! You knave! Snap out of it!"

" Sorry sir. " Shadow stated.

Misty could not help but think if what the guards said was true.. Was Shadow really Ash Ketchum? The heroic knucklehead she still loved and was waiting for..

Apparently Mrs. Ketchum had seen it too. It added up. The trouble, The heroics, the raven colored hair and the eyes. They were exactly like Ash's. As they ran up the stairs they heard the same female voice over the speaker..

"Lockdown commencing. Activating **Shadow Grid**.."

**Shadow Grid- Area where Shadow Pokemon are stronger in battle and regular Pokemon are weaker. The trainers feel pain in the Shadow Grid areas. **

As they came to the top of the stairs which reached the main foyer of the fortress, They spotted a man with short brown hair, a orange suit, brown eyes. and a sinister smile. Giovanni himself. He slowly clapped..

"Oh bravo, you two." He mocked. Eclipse growled, beginning to lose his temper. Giovanni chuckled amused.

"You need to lighten up Eclipse or should I call you.. Joel Berlitz?." Giovanni then turned to Shadow. "And as for you, Shadow.. I know your really Ash Ketchum!" Giovanni stated proud that his trap had worked better than he hoped. He chuckled again.

"And to be honest Joel, it doesn't take a psychic Pokemon to know that love and family have made you even more weak. Why you were saved I'll never know.."

"Well, If I'm so weak, Why don't you prove it? By battling me, one on one, right here, right now!" Joel stated angrily. Ash Misty and Delia looked at Joel.. Was he crazy?

"And why would I waste my time battling you?" Giovanni asked skeptically.

"Because, If you let them go," Joel gestured to the others..

"I'll put on the line my freedom and my DNA." Giovanni smiled while the others gasped.

"Well I guess I have some time to kill." Giovanni chuckled darkly.

As they stood on opposite ends of the foyer, The each held a lone poke'ball in their right hand. As they threw it they called out simultaneously..

"LET THE BATTLE BEGIN!"

I hope you enjoyed the first chapter of the rewritten version of Shadow Pokemon return. I looked back at the other one and I realized I got of track and it needed major improvements. Let me know what you think so far. Remember to Read, Review and no flames.


	2. You Just Can't Win

You Just Can't Win

I do not own any of the songs on this story. I have also modified this song so it will fit to the story.

Ash, Misty and Mrs. Ketchum proceeded to the exit. As they came to the stone bridge over the chasm the bridge exploded. Destroying their only escape route. Upon seeing several dozen rocket grunts Ash took Misty and his mother's hands and jumped to the clouds below..

With Giovanni and Joel..

The automated voice spoke again..

"Shadow grid activated.. Battlers.. Red side, King Giovanni," Joel rolled his eyes.

'_I thought my apprentice had a big ego..' _he thought.

""Challenger.. Joel Berlitz.. Please select battlefield.."

" Shadowy Ocean.." Giovanni stated. They were engulfed in purple energy. Inside they were in the ocean. It gave off the death vibe. You could see several sunken pirate ships and old cannons. There were boulders everywhere, why it looked like an earthquake had hit this place..

"Now if your done admiring the scenery.. Go Gyarados!"

Out of Giovanni's Poke'ball came a large sea serpent. It was mostly blue with yellow spots and a yellow underbelly. It had four teeth. Two on the top of it's mouth and two on it's bottom. It had purple eyes and a fin on each cheek, and on points of it's back. The Gyarados roared trying to scare him. Joel was unfazed.

"Please I've seen scarier. Ruby come on out!"

Out of Joel's Poke'ball came a Alomomola. It was a pink fish Pokemon which resembled a sideways heart. It wad a large fin on it's top and bottom and a smaller fin on it's right and left sides. It had small yellow eyes and blue marks on top of them..

With Ash Misty and Delia

As they fell Misty and Mrs. Ketchum held onto Ash.

"Ash! What were you thinking! Are you crazy!" Misty screamed.

"We'll be fine Mist! Trust me!" Ash then put his right index finger and pinky in his mouth and whistled twice. There was a sudden roar and lightning that filled the sky. Misty and Mrs. Ketchum closed their eyes terrified. They felt they had stopped falling. They also heard a familiar voice..

"Pikachupi! PiKaka!" (Misty, Mrs. Ketchum! )

"You two can open your eyes now.." Ash told them.

They were on the back of a large two footed dragon. It was mostly gray with bits of black on it. It had crimson eyes. It had a large horn on the top of it's head with a glowing blue point. It's tail was also pointed and gave off an blue electrical pulse. In Misty's arms was a familiar little pokemon. It was small yellow and had two red cheeks and a thunderbolt shaped tail. She gave the mouse a hug.

"Pikachu!"

Pikachu let out a happy "Chaa!". He knew how much Ash had missed Misty. Pikachu looked toward Ash..

_'Are you going to tell her?' _

Ash just looked to Zekrom pretending not to hear Pikachu's Aura message.

"Thanks Zekrom."

Next to Zekrom flew another dragon this one was just as big. It had light blue eyes, and white feathers. Parts of it's tail glowed a fiery orange. The top of it's head was back like hair in the wind. This dragon was called Reshiram. It turned to Ash..

"Where is your mentor young one?" She asked worriedly. Ash told of what Joel did..

"Zekrom, You know where to take them. I will meet you there." Reshiram told her brother.

"All right. Be careful Reshiram.."

With Joel and Giovanni

Giovanni and Joel began to sing. (Bold is Giovanni, Italic is Joel )

**Your way out of your league,**

**You've more than met your match..**

No words were needed in the grid. They knew what to do. Gyarados used it's bite to get Ruby in it's mouth. But Ruby used Aqua Jet to dodge and then attack from the rear.

_I guess your slowing down old man,_

_Can't hit what you can't catch,_

Gyarados then used a hyper beam dealing a great bit of damage to Ruby. Ruby then used mirror coat to do double damage at Gyarados.

**Soon the whole world will know**

**The genius of my plan**

While Gyarados could not move Ruby used Rest to restore it's health and immediately woke up..

_I will find a way to stop you_

_Anyway I can!_

**Your such a goodie two shoes!**

**It's more fun being bad!**

At this Gyarados laughed in agreement.

_I'll never side with you!_

_Your flipping mad!_

The battle was still for a moment..

**Oh yeah, What about that devastating blast?**

_That's all in the past!_

**Listen to me you whelp,**

**Nice guys finish last!**

Gyarados then attacked Ruby in a surprise attack with a Hyper Beam. Ruby used Protect to endure the hit..

_You just can't win_

**Your not that strong**

_Time to pay for your sins,_

**You've got it all wrong**

**You just can't win**

_I'm going to shut you down!_

**Your chances are slim**

_No more fooling around!_

_**Let the battle begin..**_

_**You just can't win! **_

"Gyarados Hyper Beam full power!"

"Ruby, Quick! **Protection Coat**!"

**Protection Coat- A cross of Mirror Coat and Protect. This move has the effects of Mirror Coat but greatly lessens damage done to the user. Success rate.. 30 percent.. **

As the moves collided, a cloud of smoke blocked their view..

"Ruby!" Joel shouted. He was so concerned for his Pokemon he didn't feel a thing when the hyper beam hit Ruby.

And so which Pokemon will come out still swimming? Giovanni's Deadly Gyarados? Or Joel's Sweet Alomomola, Ruby? Keep reading to find out. Remember, read and review and please no flames.

.


	3. Coming Home

Coming Home..

Karen Berlitz (OC)-47

Lily Waterflower- 21

This chapter is dedicated to Pokemonstories-crazy. My first supporter of AuraAquashipping. Your support means a lot.

Gyarados lay defeated. Ruby did a summersault smiling cheerfully. She had won her first **Shadow Battle**.

**Shadow Battle- Battle on the Shadow Grid. Very dangerous.. Risk of injury.. High.**

Joel and Giovanni returned their pokemon to their Pokeball's. Giovanni gave a evil chuckle..

"Very impressive. Your mother taught you well." What happened next stunned the young hero..

"Well, It appears I was out matched. For now." Giovanni tossed a CD case to him.

"The reward of knowledge my "Son"."

"You are no father of mine.." Joel growled. With that he left out the front gates. As he got on Reshiram, he said quietly.. "Mom, I'm coming home.." Unknown to him, Giovanni had just sent a small squadron to Cerulean..

On the outskirts of Cerulean City lay a large three story house. It was home to Karen Berlitz, Water Pokemon master now mother for twenty-one years. She had long golden hair that flowed just below her neck. She wore a purple short sleeve shirt and blue jeans. She sat at the kitchen table looking through some photos of her son. Including one that brought tears to her eyes. In it were a thirteen year old Joel and very familiar pink haired Lily Waterflower Also at thirteen. Joel was in a Cerulean blue tuxedo and had his brown hair combed to the right. He smiled and blushed as he had his right arm wrapped around Lily's waist. She wore a orange dress and had a white lily in her hair and a bright smile on her face as she rested her head on Joel's shoulder.

'They would make such a cute couple' she thought. A knock at the door caught her attention. As she opened it, There was Lily. She had been crying. Lily tried to smile. Mrs. Berlitz had become a something of a second mother to Lily, Daisy and Violet. Thanks to her, The oldest sisters could run the gym with out relying on Misty to battle. They were currently ranked second only after the Saffron gym.

Karen led Lily inside where they sat on the couch. Joel had been gone for seven years.

"Next week is.." Lily started. She longed to tell him how she felt but was to afraid. Karen embraced her in a motherly hug.

"Christmas.. I know. I miss him too."

"I never told him.." Lily started.. Karen smiled.

"You love him." Lily nodded. They were unaware of what was happening outside..

"Thanks for the help Reshiram. I got it from here." The dragon of truth smiled and rolled her eyes and took off. As Joel stepped up to the house he noticed his mother had got some new decorations. The driveway and pathway to the house were lined with light up candy canes. As he entered his mother and Lily were unaware of his entrance. It was time for a Christmas miracle..

" Are those candy canes edible?" he asked smiling. It was one of those moments where time seemed to stand still. Karen and Lily turned around. There he was. He stood there smiling. His mother and Lily came up to him. Karen approached her son and looked him in the eyes. Those blue beast like eyes..

"Joel?" She whispered, tears in her eyes. He whispered in her ear what he told her when he was little..

"I wanna be like you someday mommy." Karen hugged her son tightly.

"My son's alive! Thank the ancestors!"

"Mom! Can't breathe!" He gasped. Once his mother let go Lily embraced him. He wasn't expecting this. But he gladly returned it. He looked at his mother.. She nodded and headed into the Kitchen. Once she was gone Joel whispered to Lily..

"I love you so much Lily.. I have for a while." She whispered to him.

"I love you too. I really missed you." She then gave her new boyfriend a passionate kiss on the lips which he gladly returned.

Karen had finished setting the table for dinner. It was a Christmas miracle. Her son had come home after seven years. As she came into the living room, She found her son and Lily in a kiss. Karen smiled at the sight. She stepped back into the kitchen smiling. Her son was in love.. Not long after Joel and Lily entered the room smiling. Once he saw the spread his mother had prepared he smiled.

"I thought I smelled something burning." His mother couldn't help but laugh at the jab at her cooking. She missed his humor. He then grabbed his bag and put down five bowls of pokemon food.

"Dinner everyone!"

Out of his Pokeball's came Ruby, Storm, Gawain, (a Lucario) , Lily (a Milotic) and Tricky (a Keldeo).

Joel's mother and Lily were impressed by Joel's pokemon. They were well taken care of. When his mother asked Joel why Tricky trusted him so much, Joel simply said..

"We are very much alike.."

What did Joel mean by that? Next chapter is with Ash, Misty and Delia. I also need episode ideas for Kanto chronicles. Remember. Read review and please no flames.


	4. Joel's Truth, Lords of Fear and Thunder

Joel's Truth, Lords of Fear and Thunder

Ash had thought the plan was simple. But unfortunatly, every plan tends to get complicated at some point. This was that point.. His eyes turned blue as he was having an **Aura Vision**.

**Aura Vision- A vision of the future or past that only certain Guardians can see. Can usually be triggered by a object.**

Ash's Vision

He saw Cerulean in ruins.. Houses were burned to the ground. Team Rocket had perfected their newest shadow weapon.. The **Shadow Disk..**

**Shadow Disk- A light wearable disk, It captures wild Pokemon as well as has a Shadow Grid feature.. **

End Vision..

" Zekrom.. We need to get to Joel's hometown.. Now!" Ash said with utmost urgency.

" Ash? For you to go against your mentors orders is new.. I sense you just had an awful vision.." Zekrom said gravely. Delia, and Misty just looked stunned. Pikachu as well only on the count of Ash disobeying Joel's orders..

They set off immediately for Cerulean City..

Joel, His mother and Lily, went into the living room. It was the first time Joel noticed the tree. It was decorated with different Pokemon ornaments he gave his mother over the few years... From Staryu and Teddiursa and even Eevee and Vaporeon. They were all here.. Even the Starmie tree star ornament.. Yet there was not the smell of the tree that he was allergic to.. He looked at his mother in confusion.

"I got a fake tree the year you disappeared. I put the ornaments on with Lily and her sisters." Lily couldn't help but blush as she remembered she was still holding her new boyfriend's hand.

"Get down!"

Joel immediately pushed his mother and Lily to the ground protecting them from a large Dark Pulse attack as it came through the window. Glass cutting through Joel's shirt and getting stuck in his back..

Ash and the others had seen the attack and went in for a closer look. Misty then realized where they were..

As Karen and Lily looked at Joel, they noticed he was struggling to get up, and yet he was smiling..

"(Cough).. I thought I smelled an ape.." Joel chuckled. Out of the dust came Rocket administrator Gorigan. He was a middle aged man with the posture of a gorilla. He wore a red tank top, goggles and brown army pants. He wore an angry expression that could scare a Nidoking.

"You always did have a big mouth punk.." He outstretched his arm revealing a purple disk. On it was a small red R and six poke ball slots. Gorigan chuckled evilly when he saw the slight fear in Joel's eyes.

" Yes, this is the **Shadow Disk** we had under development. Any Pokemon we catch will be transformed into a Shadow Pokemon. And it is finally completed. What's better it even has.. Well, perhaps I'll just show you.." he pushed one of it's buttons activating the **Shadow Grid**. They were surrounded by holographic tombstones and memorials. A white fog hovered just above the ground.

" Welcome "**Project Aura**" to the **Shadow Cemetery.**" Gorigan laughed. Joel happened to see Ash and the others on Zekrom and motioned for them to move on into Cerulean. Ash nodded. Lily and Misty caught each other's eyes. The look in Lily's eyes told Misty that Ash needed help through this just as Joel did..

**Project Aura- Also known as Joel Berlitz , He was taken from his birth parents due to something only he knows. Only two months later was rescued by his now adoptive mother, Karen Berlitz. At the age of five, he became close friends with Daisy, Lily, and Violet Waterflower. Lily fell in love with him at ten years old. When he turned ten, Joel became a water Pokemon trainer just like his mother. (with a few exceptions) He then mysteriously disappeared at the age of thirteen. Despite the horrible truth he learned, He remains pure of heart and chivalrous. He always does his best to help those in need. **

**Karen Berlitz- A retired water Pokemon master, She is also Joel's adoptive mother. After the early death of her husband twenty two years ago she started working in his place to bring down Team Rocket. During a mission, She came across a baby called Project Aura. She adopted the baby boy and returned to normal life to raise the child as her own. **

**Lily Waterflower- One of the four Cerulean Sisters, She was Joel's best friend, now girlfriend. She, her sister's Daisy, and Violet have known Joel since childhood. Normally kind and sweet, many know not to anger her. Otherwise they will see that Misty is not the only Waterflower to be feared. **

**Shadow Cemetery- This location powers up dark, and ghost Pokemon and their moves by two levels. It powers down Psychic and Fighting types by two levels..**

Zekrom had landed outside of the Cerulean gym. Once Ash had gotten off, Misty did the same.

" Misty.." Ash started but was cut off by the redhead..

"Ash Ketchum this is where I was born and I will defend it." she told him. Ash put his hand to his head.

"Misty, you don't understand.." She started to counter but Ash put his hand over her mouth to keep her quiet.

" In these battles, you feel the pain your Pokemon feels. I care about you too much to lose you again." he was trying his best to hold in alone tear. Misty wiped it away and held Ash's hands.. She whispered lovingly.. (an emotion that Ash caught)

" I'm with you however it ends.."

The two walked hand in hand into the gym not knowing the foe would be Ash's most dangerous yet..

I decided to keep the lord of thunder a secret.. For now. I hope you like the entries I put in bold . I decided to call it.. The Auradex.. From now on key characters and location and such will be explaind in the Auradex. And yes. Ash and Misty are together. Contrustive reviews are always welcome. But please no flames.


End file.
